Research workbench
NAD complex structure of PH1275 protein from pyrococcus horikoshii
Analyse NAD complex structure of PH1275 protein from pyrococcus horikoshii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DVM
- Type
- protein
- Length
- 1,746 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 439AA long hypothetical malate oxidoreductase
- EC
- 1.1.1.38
- UniProt
- O59029
- Ligands
- NAD
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 439AA long hypothetical malate oxidoreductase (EC 1.1.1.38) | protein | 438 | 48% helix, 13% strand | O59029 |
| B | 439AA long hypothetical malate oxidoreductase (EC 1.1.1.38) | protein | 434 | 48% helix, 13% strand | O59029 |
| D | 439AA long hypothetical malate oxidoreductase (EC 1.1.1.38) | protein | 436 | 49% helix, 13% strand | O59029 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.77 | 0.80 | 76 | NAD |
| 2 | 1109 | 0.77 | 0.79 | 80 | MES |
| 3 | 967 | 0.77 | 0.79 | 94 | MES |
| 4 | 889 | 0.76 | 0.79 | 72 | NAD |
| 5 | 841 | 0.76 | 0.79 | 71 | NAD |
Interfaces
4 interfaces between chains.
- C–D · 5347 Ų buried · 70 hydrogen bonds · protein-protein
- A–B · 5239 Ų buried · 71 hydrogen bonds · protein-protein
- A–C · 969 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 40 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2DVM · NAD complex structure of PH1275 protein from Pyrococcus horikoshii · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O59029
- Elsewhere: RCSB PDB 2DVM · PDBe 2DVM · UniProt O59029
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